This analysis is based on the single-cell RNA-seq dataset published in:
Tu, J. et al. (2021). Single-Cell Transcriptomics of Human Nucleus Pulposus Cells: Understanding Cell Heterogeneity and Degeneration. Advanced Science, 8(23), 2103631. https://doi.org/10.1002/advs.202103631
From the plots generated: - UMAP/tSNE: Reveal 6 biologically interpretable NPC subtypes. - DotPlot: Confirms canonical marker expression in annotated subtypes. - Pseudotime: Suggests HT-CLNPs are early progenitors transitioning into mature states such as effector or fibroNPCs.
This analysis use dataset “GSE165722”.
QC Violin Plot
UMAP Clusters
tSNE Clusters by Cell Type
## p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene
## 1 0 1.8229819 0.868 0.317 0 0 CYR61
## 2 0 1.2440728 0.977 0.431 0 0 DCN
## 3 0 1.8586392 0.877 0.345 0 0 CTGF
## 4 0 1.3793767 0.947 0.417 0 0 LUM
## 5 0 1.7458917 0.940 0.456 0 0 FN1
## 6 0 0.6984552 0.915 0.438 0 0 CLU
Top Marker DotPlot
Cell Type Distribution Barplot
Pseudotime trajectory of NPC populations
.counts.tsv.gz and
.cellname.txt.gz pairs are expected in
data/GSE165722/extracted/filtered_feature_bc_matrix/
directories for each sample. ## 📊 Additional Static Results